[2024-01-24 12:06:35,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:35,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:35,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference
[2024-01-24 12:06:36,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:36,525] [INFO] Task started: Prodigal
[2024-01-24 12:06:36,526] [INFO] Running command: gunzip -c /var/lib/cwl/stg32b08f95-f2b8-49c7-a427-29772b2c8cd2/GCF_003259435.1_ASM325943v1_genomic.fna.gz | prodigal -d GCF_003259435.1_ASM325943v1_genomic.fna/cds.fna -a GCF_003259435.1_ASM325943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:11,987] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:11,988] [INFO] Task started: HMMsearch
[2024-01-24 12:07:11,988] [INFO] Running command: hmmsearch --tblout GCF_003259435.1_ASM325943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference/reference_markers.hmm GCF_003259435.1_ASM325943v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:12,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:12,333] [INFO] Found 6/6 markers.
[2024-01-24 12:07:12,393] [INFO] Query marker FASTA was written to GCF_003259435.1_ASM325943v1_genomic.fna/markers.fasta
[2024-01-24 12:07:12,394] [INFO] Task started: Blastn
[2024-01-24 12:07:12,394] [INFO] Running command: blastn -query GCF_003259435.1_ASM325943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference/reference_markers.fasta -out GCF_003259435.1_ASM325943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:12,985] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:12,989] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:12,990] [INFO] Target genome list was writen to GCF_003259435.1_ASM325943v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:12,996] [INFO] Task started: fastANI
[2024-01-24 12:07:12,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b08f95-f2b8-49c7-a427-29772b2c8cd2/GCF_003259435.1_ASM325943v1_genomic.fna.gz --refList GCF_003259435.1_ASM325943v1_genomic.fna/target_genomes.txt --output GCF_003259435.1_ASM325943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:33,450] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:33,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:33,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:33,465] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:33,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:33,465] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Chitinophaga dinghuensis	strain=DSM 29821	GCA_003259435.1	1539050	1539050	type	True	100.0	2360	2360	95	conclusive
Chitinophaga jiangningensis	strain=DSM 27406	GCA_900142605.1	1419482	1419482	type	True	80.7398	945	2360	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	79.2134	659	2360	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	79.056	576	2360	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	79.0219	617	2360	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	78.9122	601	2360	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	78.9034	646	2360	95	below_threshold
Chitinophaga niastensis	strain=DSM 24859	GCA_003014755.1	536980	536980	type	True	78.8946	584	2360	95	below_threshold
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	78.8766	573	2360	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	78.7742	601	2360	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	78.7568	666	2360	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	78.7304	572	2360	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	77.5995	270	2360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,467] [INFO] DFAST Taxonomy check result was written to GCF_003259435.1_ASM325943v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:33,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:33,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:33,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference/checkm_data
[2024-01-24 12:07:33,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:33,538] [INFO] Task started: CheckM
[2024-01-24 12:07:33,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259435.1_ASM325943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259435.1_ASM325943v1_genomic.fna/checkm_input GCF_003259435.1_ASM325943v1_genomic.fna/checkm_result
[2024-01-24 12:09:08,873] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:08,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:08,903] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:08,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:08,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259435.1_ASM325943v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:08,904] [INFO] Task started: Blastn
[2024-01-24 12:09:08,904] [INFO] Running command: blastn -query GCF_003259435.1_ASM325943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502a52c3-cbde-4a9e-a443-4b331eab1814/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259435.1_ASM325943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:09,677] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:09,682] [INFO] Selected 10 target genomes.
[2024-01-24 12:09:09,682] [INFO] Target genome list was writen to GCF_003259435.1_ASM325943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:09,707] [INFO] Task started: fastANI
[2024-01-24 12:09:09,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b08f95-f2b8-49c7-a427-29772b2c8cd2/GCF_003259435.1_ASM325943v1_genomic.fna.gz --refList GCF_003259435.1_ASM325943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259435.1_ASM325943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:24,259] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:24,274] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:24,274] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003259435.1	s__Chitinophaga dinghuensis	100.0	2360	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019236475.1	s__Chitinophaga sp019236475	86.298	1690	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142605.1	s__Chitinophaga jiangningensis	80.7491	944	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019219075.1	s__Chitinophaga sp019219075	80.641	971	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752935.1	s__Chitinophaga sp011752935	80.6158	1011	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001870995.2	s__Chitinophaga sp001870995	80.483	916	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167635.1	s__Chitinophaga vietnamensis	79.2166	659	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900168065.1	s__Chitinophaga ginsengisegetis	78.8652	575	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.27	98.27	0.94	0.94	3	-
GCF_900110835.1	s__Chitinophaga arvensicola	78.7564	604	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150045.1	s__Chitinophaga polysaccharea_A	78.7493	528	2360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	96.96	96.96	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:24,276] [INFO] GTDB search result was written to GCF_003259435.1_ASM325943v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:24,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:24,280] [INFO] DFAST_QC result json was written to GCF_003259435.1_ASM325943v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:24,280] [INFO] DFAST_QC completed!
[2024-01-24 12:09:24,280] [INFO] Total running time: 0h2m49s